Jul2009 ontology report

Ontology Development & GO Editorial Office Report - July 2009

I. Ontology Development

• SourceForge
  • Items opened: 86
  • Items closed: 68 (3 duplicates deleted)
  • Items still open: 257
    • assigned, GO Eds: 92
    • assigned, MOD curators: 115
    • unassigned: 50

• Content items resolved
  • The has_part relation has been implemented in the CC ontology (and will soon be used in BP also).
    • Background
    • Documentation is available (thanks to Amelia)
    • SF item on spliceosomes for which new terms have been added, using has_part
  • Several SourceForge items resolved

• Content items in progress
  • The plan to add internal cross-products to the go_write (and therefore also go_ext) file is in progress.
  • Work has begun on terms for kidney development
  • New terms from SDB meeting (see below)
  • Evaluating new link suggestions and mismatches from ChEBI cross-products
  • Continuing to add function-process part-of links in gene_ontology_write.obo and gene_ontology_ext.obo
  • Work continues on overhauling terms related to viruses
  • Signal transduction overhaul is going very well; see Signaling_Meeting_Minutes_July_2009 for latest notes (Jen and experts including Sandra Orchard)
  • Also continuing
    • Additional progress on Cellular component organization and biogenesis, in light of internal cross-products
    • Taxon triggers; currently moving "sensu" information from synonyms to definitions (see notes for latest)
      • Work on branching organ development (David)
  • Quality control continues as usual - reports generated by Chris
    • Regulation - also see above (David, Tanya)
    • Multiple part_of parents (several GO curators, especially Tanya & David)
  • Various SourceForge items

• Manuscript in preparation for paper on the regulates relationships should resume soon (Midori & Jane so far; David, Chris and Tanya to join in)
• Considering publication options for cross-product paper (extended version of ICBO xp work noted below)

• Meetings
  • ICBO, Buffalo, NY July 20-23
    • Cross-product talk and paper (Chris et al.); see http://precedings.nature.com/documents/3496/version/1
    • OBO-Edit demos (Amina, David OS)
  • David and Tanya attended the Society for Developmental Biology meeting (San Francisco, July 23-27), and have begun adding ontology terms based on discussions with other participants. They expect to add about 50-100 terms.
  • Organization under way for September GOC and SAB meetings

• Reminder: plan to retire .ontology file format August 1st - see Managers_21Jan09 and GO_Timeline

See monthly report in CVS for ontology statistics.

II. GO Editorial Office activities not represented in part I

• OBO-Edit working group:
  • OBO-Edit 2.1 beta released for testing
  • See meeting minutes from July 1 and 16, and monthly report
  • ICBO presentations (see above)

• Advocacy/outreach (Jane, Jen)
  • See monthly report

• Anything else
  • GO bibliography has 2797 entries

Back to list